NPASS Compound

Structure

NPC276262 OpenBabel06302215422D 29 33 0 0 1 0 0 0 0 0999 V2000 -0.9511 -1.6910 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.8171 -1.1910 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.6831 -1.6910 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.6831 -2.6910 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.5491 -3.1910 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.4152 -2.6910 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.4152 -1.6910 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.5491 -1.1910 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.5491 -0.1910 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -2.6831 0.3090 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.8171 -0.1910 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.9511 0.3090 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.9511 1.3090 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.8171 1.8090 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.6831 1.3090 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.5491 1.8090 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.4152 1.3090 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -5.3662 1.6180 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.9540 0.8090 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -5.3662 -0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.6752 -0.9511 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -4.4152 0.3090 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -0.0000 1.6180 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.5878 0.8090 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 0.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -5.2812 -3.1910 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -6.1472 -2.6910 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.5491 -4.1910 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.6831 -4.6910 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1 2 1 0 0 0 0 2 3 1 0 0 0 0 3 8 2 0 0 0 0 3 4 1 0 0 0 0 4 5 2 0 0 0 0 5 6 1 0 0 0 0 5 28 1 0 0 0 0 6 7 2 0 0 0 0 6 26 1 0 0 0 0 7 8 1 0 0 0 0 9 8 1 1 0 0 0 9 10 1 0 0 0 0 9 22 1 0 0 0 0 10 15 2 0 0 0 0 10 11 1 0 0 0 0 11 12 2 0 0 0 0 12 25 1 0 0 0 0 12 13 1 0 0 0 0 13 14 2 0 0 0 0 13 23 1 0 0 0 0 14 15 1 0 0 0 0 15 16 1 0 0 0 0 17 16 1 6 0 0 0 17 18 1 0 0 0 0 17 22 1 0 0 0 0 18 19 1 0 0 0 0 19 20 1 0 0 0 0 20 21 2 0 0 0 0 22 20 1 6 0 0 0 23 24 1 0 0 0 0 24 25 1 0 0 0 0 26 27 1 0 0 0 0 28 29 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	398.14
Volume:	389.362
LogP:	3.043
LogD:	3.111
LogS:	-4.977
# Rotatable Bonds:	4
TPSA:	72.45
# H-Bond Aceptor:	7
# H-Bond Donor:	0
# Rings:	5
# Heavy Atoms:	7

MedChem Properties

QED Drug-Likeness Score:	0.733
Synthetic Accessibility Score:	3.546
Fsp3:	0.409
Lipinski Rule-of-5:	Accepted
Pfizer Rule:	Rejected
GSK Rule:	Accepted
BMS Rule:	0
Golden Triangle Rule:	Accepted
Chelating Alert:	0
PAINS Alert:	0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-5.007
MDCK Permeability:	5.4473475756822154e-05
Pgp-inhibitor:	0.705
Pgp-substrate:	0.0
Human Intestinal Absorption (HIA):	0.001
20% Bioavailability (F20%):	0.011
30% Bioavailability (F30%):	0.049

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.139
Plasma Protein Binding (PPB):	94.22603607177734%
Volume Distribution (VD):	1.445
Pgp-substrate:	4.702772617340088%

ADMET: Metabolism

CYP1A2-inhibitor:	0.194
CYP1A2-substrate:	0.97
CYP2C19-inhibitor:	0.936
CYP2C19-substrate:	0.919
CYP2C9-inhibitor:	0.7
CYP2C9-substrate:	0.834
CYP2D6-inhibitor:	0.28
CYP2D6-substrate:	0.912
CYP3A4-inhibitor:	0.952
CYP3A4-substrate:	0.923

ADMET: Excretion

Clearance (CL):	13.406
Half-life (T1/2):	0.208

ADMET: Toxicity

hERG Blockers:	0.106
Human Hepatotoxicity (H-HT):	0.16
Drug-inuced Liver Injury (DILI):	0.906
AMES Toxicity:	0.131
Rat Oral Acute Toxicity:	0.18
Maximum Recommended Daily Dose:	0.956
Skin Sensitization:	0.08
Carcinogencity:	0.424
Eye Corrosion:	0.003
Eye Irritation:	0.06
Respiratory Toxicity:	0.854

Download Data

Data Type	Select
General Info & Identifiers & Properties
Structure MOL file
Source Organisms
Biological Activities
Similar NPs/Drugs

Natural Product: NPC276262

Natural Product ID:	NPC276262
*Common Name:**	TUGXVGMIXLPLHW-QDEDPJFRSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	TUGXVGMIXLPLHW-QDEDPJFRSA-N
Standard InCHI:	InChI=1S/C22H22O7/c1-24-15-8-17(26-3)16(25-2)7-14(15)21-13-6-19-18(28-10-29-19)5-11(13)4-12-9-27-22(23)20(12)21/h5-8,12,20-21H,4,9-10H2,1-3H3/t12-,20+,21-/m0/s1
SMILES:	COc1cc(c(cc1[C@@H]1c2cc3c(cc2C[C@H]2COC(=O)[C@@H]12)OCO3)OC)OC
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	56841131
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0001392] Lignans, neolignans and related compounds [CHEMONTID:0001510] Lignan lactones

*Note: the InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
**Note: the Chemical Classification was calculated by NPClassifier Version 1.5. Reference: PMID:34662515.

Species Source

Organism ID	Organism Name	Taxonomy Level	Family	SuperKingdom	Isolation Part	Collection Location	Collection Time	Reference
NPO3987	Syzygium aromaticum	Species	Myrtaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[1402962]
NPO28256	Platycladus orientalis	Species	Cupressaceae	Eukaryota	Leaves and branches	Soorkesh Valley, Gollestan, Iran	n.a.	PMID[15104493]
NPO28256	Platycladus orientalis	Species	Cupressaceae	Eukaryota	leaves	Soorkesh Valley, Gollestan, Iran	n.a.	PMID[15104493]
NPO14484	Echinacea purpurea	Species	Asteraceae	Eukaryota	root	n.a.	n.a.	PMID[15921428]
NPO14484	Echinacea purpurea	Species	Asteraceae	Eukaryota	flowers	n.a.	n.a.	PMID[19374389]
NPO8528	Citrus junos	Species	Rutaceae	Eukaryota	n.a.	fruit	n.a.	PMID[25522543]
NPO3987	Syzygium aromaticum	Species	Myrtaceae	Eukaryota	Flower Buds	n.a.	n.a.	PMID[26977531]
NPO3987	Syzygium aromaticum	Species	Myrtaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[8904847]
NPO3987	Syzygium aromaticum	Species	Myrtaceae	Eukaryota	Bark	n.a.	n.a.	Database[FooDB]
NPO3987	Syzygium aromaticum	Species	Myrtaceae	Eukaryota	Essential Oil	n.a.	n.a.	Database[FooDB]
NPO3987	Syzygium aromaticum	Species	Myrtaceae	Eukaryota	Fruit	n.a.	n.a.	Database[FooDB]
NPO3987	Syzygium aromaticum	Species	Myrtaceae	Eukaryota	Leaf	n.a.	n.a.	Database[FooDB]
NPO3987	Syzygium aromaticum	Species	Myrtaceae	Eukaryota	Stem	n.a.	n.a.	Database[FooDB]
NPO3987	Syzygium aromaticum	Species	Myrtaceae	Eukaryota		n.a.	n.a.	Database[FooDB]
NPO3987	Syzygium aromaticum	Species	Myrtaceae	Eukaryota	n.a.	n.a.		Database[FooDB]
NPO8528	Citrus junos	Species	Rutaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO8952	Craibiodendron yunnanese	Species	Ericaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO21685	Magnolia coco	Species	Magnoliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO14484	Echinacea purpurea	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO8367	Fructus schiandrae	n.a.	n.a.	n.a.	n.a.	n.a.	n.a.	Database[HerDing]
NPO10608	Exodermis poria	n.a.	n.a.	n.a.	n.a.	n.a.	n.a.	Database[HerDing]
NPO3987	Syzygium aromaticum	Species	Myrtaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO8367	Fructus schiandrae	n.a.	n.a.	n.a.	n.a.	n.a.	n.a.	Database[TCMID]
NPO7510	Ixora chinensis	Species	Rubiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO8528	Citrus junos	Species	Rutaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO28256	Platycladus orientalis	Species	Cupressaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO10608	Exodermis poria	n.a.	n.a.	n.a.	n.a.	n.a.	n.a.	Database[TCMID]
NPO3987	Syzygium aromaticum	Species	Myrtaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO8952	Craibiodendron yunnanese	Species	Ericaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO21685	Magnolia coco	Species	Magnoliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO14484	Echinacea purpurea	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO3608	Eleutherococcus giraldii	Species	Araliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO21685	Magnolia coco	Species	Magnoliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO28256	Platycladus orientalis	Species	Cupressaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO3987	Syzygium aromaticum	Species	Myrtaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO3987	Syzygium aromaticum	Species	Myrtaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO28256	Platycladus orientalis	Species	Cupressaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO3987	Syzygium aromaticum	Species	Myrtaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO28256	Platycladus orientalis	Species	Cupressaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO3608	Eleutherococcus giraldii	Species	Araliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO7510	Ixora chinensis	Species	Rubiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO14484	Echinacea purpurea	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO8528	Citrus junos	Species	Rutaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO21685	Magnolia coco	Species	Magnoliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]

☑ Note for Reference:
In addition to directly collecting NP source organism data from primary literature (where reference will provided as NCBI PMID or DOI links), NPASS also integrated them from below databases:
☉ UNPD: Universal Natural Products Database [PMID: 23638153].
☉ StreptomeDB: a database of streptomycetes natural products [PMID: 33051671].
☉ TM-MC: a database of medicinal materials and chemical compounds in Northeast Asian traditional medicine [PMID: 26156871].
☉ TCM@Taiwan: a Traditional Chinese Medicine database [PMID: 21253603].
☉ TCMID: a Traditional Chinese Medicine database [PMID: 29106634].
☉ TCMSP: The traditional Chinese medicine systems pharmacology database and analysis platform [PMID: 24735618].
☉ HerDing: a herb recommendation system to treat diseases using genes and chemicals [PMID: 26980517].
☉ MetaboLights: a metabolomics database [PMID: 27010336].
☉ FooDB: a database of constituents, chemistry and biology of food species [www.foodb.ca].

NP Quantity Composition/Concentration

Organism ID	NP ID	Organism Material Preparation	Organism Part	NP Quantity (Standard)	NP Quantity (Minimum)	NP Quantity (Maximum)	Quantity Unit	Reference

☑ Note for Reference:
In addition to directly collecting NP quantitative data from primary literature (where reference will provided as NCBI PMID or DOI links), NPASS also integrated NP quantitative records for specific NP domains (e.g., NPS from foods or herbs) from domain-specific databases. These databases include:
☉ DUKE: Dr. Duke's Phytochemical and Ethnobotanical Databases.
☉ PHENOL EXPLORER: is the first comprehensive database on polyphenol content in foods [PMID: 24103452], its homepage can be accessed at here.
☉ FooDB: a database of constituents, chemistry and biology of food species [www.foodb.ca].

Biological Activity

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference

☑ Note for Activity Records:
☉ The quantitative biological activities were primarily integrated from ChEMBL (Version-30) database and were also directly collected from PubMed literature. PubMed PMID was provided as the reference link for each activity record.

Chemically structural similarity: I. Similar Active Natural Products in NPASS

Top-200 similar NPs were calculated against the active-NP-set (includes 4,3285 NPs with experimentally-derived bioactivity available in NPASS)

Similarity level is defined by Tanimoto coefficient (Tc) between two molecules. Tc lies between [0, 1] where '1' indicates the highest similarity. What is Tanimoto coefficient

● The left chart: Distribution of similarity level between NPC276262 and all remaining natural products in the NPASS database.
● The right table: Most similar natural products (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	407
0.1-0.2	1658
0.2-0.3	3410
0.3-0.4	8161
0.4-0.5	10729
0.5-0.6	4241
0.6-0.7	8673
0.7-0.8	5033
0.8-0.85	272
0.85-0.9	75
0.9-0.95	28
0.95-1	10

Similarity Score	Similarity Level	Natural Product ID

Chemically structural similarity: II. Similar Clinical/Approved Drugs

Similarity level is defined by Tanimoto coefficient (Tc) between two molecules.

● The left chart: Distribution of similarity level between NPC276262 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	350
0.1-0.2	891
0.2-0.3	1788
0.3-0.4	2774
0.4-0.5	1906
0.5-0.6	921
0.6-0.7	448
0.7-0.8	60
0.8-0.85	8
0.85-0.9	0
0.9-0.95	4
0.95-1	0

Similarity Score	Similarity Level	Drug ID	Developmental Stage

Bioactivity similarity: Similar Natural Products in NPASS

Bioactivity similarity was calculated based on bioactivity descriptors of compounds. The bioactivity descriptors were calculated by a recently developed AI algorithm Chemical Checker (CC) [Nature Biotechnology, 38:1087–1096, 2020; Nature Communications, 12:3932, 2021], which evaluated bioactivity similarities at five levels:
☉ A: chemistry similarity;
☉ B: biological targets similarity;
☉ C: networks similarity;
☉ D: cell-based bioactivity similarity;
☉ E: similarity based on clinical data.

Those 5 categories of CC bioactivity descriptors were calculated and then subjected to manifold projection using UMAP algorithm, to project all NPs on a 2-Dimensional space. The current NP was highlighted with a small circle in the 2-D map. Below figures: left-to-right, A-to-E.

A: chemistry similarity

B: biological targets similarity

C: networks similarity

D: cell-based bioactivity similarity

E: similarity based on clinical data